Gene detail

Detailed information of OS493_030810-T1 in Lophelia pertusa

Genomic Location: scaffold_203:96404...108893
NR annotation: KAJ7353967.1, GTPase-activating protein S13 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3ZCC9	Protein SEC13 homolog OS=Bos taurus OX=9913 GN=SEC13 PE=2 SV=1
P55735	Protein SEC13 homolog OS=Homo sapiens OX=9606 GN=SEC13 PE=1 SV=3
Q9D1M0	Protein SEC13 homolog OS=Mus musculus OX=10090 GN=Sec13 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004398 (this species only)
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR037363 all species →	Family	Sec13/Seh1 family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11024 all species →	NUCLEAR PORE COMPLEX PROTEIN SEC13 / SEH1 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005198 all species →	Molecular Function	structural molecule activity	Interproscan
GO:0006606 all species →	Biological Process	protein import into nucleus	Interproscan
GO:0030127 all species →	Cellular Component	COPII vesicle coat	Interproscan
GO:0031080 all species →	Cellular Component	nuclear pore outer ring	Interproscan
GO:0032008 all species →	Biological Process	positive regulation of TOR signaling	Interproscan
GO:0032527 all species →	Biological Process	protein exit from endoplasmic reticulum	Interproscan
GO:0090114 all species →	Biological Process	COPII-coated vesicle budding	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for OS493_030810-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_030810-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

110TPM > 0

7Conditions

100.4Max TPM

40.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	36.06	49.68
polyp at pH7 6	18	18	45.27	100.45
coral polyp · control treatment	16	16	42.22	63.16
coral polyp · oil and dispersant treatment	16	16	40.42	60.25
coral polyp · oil treatment	16	16	35.25	45.10
coral polyp · dispersant treatment	16	16	34.26	44.52
Polyp	10	10	53.23	96.09

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.68
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.22
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.20
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.05
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.77
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.54
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.72
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.11
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.59
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.94
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.97
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.07
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.05
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.05
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.42
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.82
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.55
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	100.45
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	96.94
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.55
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.43
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.12
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.70
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.23
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.21
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.53
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.31
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.63
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.62
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.41
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.72
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.90
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.52
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.41
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.10
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.16
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.88
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.66
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.39
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.11
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.55
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.75
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.01
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.86
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.46
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.01
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.07
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.64
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.66
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.35
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.97
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.25
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.20
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.07
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.59
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.82
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.43
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.30
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.68
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.39
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.29
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.76
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.89
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.56
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.64
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.68
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.11
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.10
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.47
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.26
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.31
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.86
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.32
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.71
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.01
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.26
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.76
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.95
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.84
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.24
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.43
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.17
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.52
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.86
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.42
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.02
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.81
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.88
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.63
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.62
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.45
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.49
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.83
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.82
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.50
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.37
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.71
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	96.09
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	74.06
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	61.73
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	56.28
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	54.15
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	47.11
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	43.37
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	41.71
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	37.89
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	19.88

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.